Re: Proposed addition to L3 core
08 Sep '09 09:22
On Tue, 08 Sep 2009 11:48:24 -0400
Oliver Ruebenacker <firstname.lastname@example.org> wrote:
> Hello Stefan, All,
> I don't know what confusion you are talking about or why you think
> you need to state the obvious, that SBML is about modelling. I also
> don't understand why you repeat Nicolas' argument that compartments
> are special because they have a number associated with it, while
> ignoring my response to that. I am sure we can add some number to
> entities as well.
You have several species in the same compartment thus having a
compartment entity facilitates normalization. Your alternative would
require manual synchronization of the compartment size for all species
in the same compartment.
> It surprises me that, after even Nicolas conceded the weakness of
> MIRIAM annotations, you still insist they are perfect and only
> "cumbersome". If you think that, then please provide examples how to
> annotate variant sequences, post-translational modifications and
> different complex formations.
I did not say at all that the way MIRIAM annoation is implemented in
SBML is good. In fact I am one of the harshes critics. However any
grouping mechanism will require the group to be annotated with MIRIAM
information to identify the group in a MIRIAM complian way. We all know
that names are not an option. Thus MIRIAM annotation will be part of the
final solution. Improving the capabilities of providing MIRIAM compliant
annotation is another problem.
> If a species is a pool of indistinguishable things, it is only
> natural that two species that contain the same indistinguishable
> things have a unique relationship and therefore require a unique way
> of being grouped.
The above is a logically wrong statement. How can two indistinguishable
things be distinguishable. It seems that my attempt to remove confusion
was not sufficient though you claim that there is no need for this ;)
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility II
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
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